Abstract
Biological knowledge has been, to date, coded by biologists in axiomatically lean bio-ontologies. To facilitate axiomatic enrichment, complex semantics can be encapsulated as Ontology Design Patterns (ODPs). These can be applied across an ontology to make the domain knowledge explicit and therefore available for computational inference. The same ODP is often required in many different parts of the same ontology and the manual construction of often complex ODP semantics is loaded with the possibility of slips, inconsistencies and other errors. To address this issue we present the Ontology PreProcessor Language (OPPL), an axiom-based language for selecting and transforming portions of OWL ontologies, offering a means for applying ODPs. Example ODPs for the common need to represent “modifiers” of independent entities are presented and one of them is used as a demonstration of how to use OPPL to apply it.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Bodenreider, O., Stevens, R.: Bio-ontologies: current trends and future directions. Brief. Bioinformatics 7(3), 256–274 (2006)
Pressuti, V., Gangemi, A., David, S., de Cea, G.A., Suárez-Figueroa, M., Montiel-Ponsoda, E., Poveda, M.: A Library of Ontology Design Patterns. NeOn Deliverable 2.5.1 (2008)
Egaña, M., Antezana, E., Stevens, R.: Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language. In: OWLed. (2008)
Gangemi, A.: Ontology Design Patterns for Semantic Web Content. In: Gil, Y., Motta, E., Benjamins, V.R., Musen, M.A. (eds.) ISWC 2005. LNCS, vol. 3729, pp. 262–276. Springer, Heidelberg (2005)
Aranguren, M.E., Antezana, E., Kuiper, M., Stevens, R.: Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. BMC bioinformatics 9 (suppl. 5), S1 (2008)
Brockmans, S., Volz, R., Eberhart, A., Löffler, P.: Visual Modelling of OWL DL Ontologies using UML. In: McIlraith, S.A., Plexousakis, D., van Harmelen, F. (eds.) ISWC 2004. LNCS, vol. 3298, pp. 198–213. Springer, Heidelberg (2004)
Grenon, P., Smith, B., Goldberg, L.: Biodynamic Ontology: Applying BFO in the Biomedical Domain. In: Pisanelli, D.M. (ed.) Ontologies in Medicine, pp. 20–38. IOS Press, Amsterdam (2004)
Gangemi, A., Guarino, N., Masolo, C., Oltramari, A., Schneider, L.: Sweetening ontologies with DOLCE. In: Gómez-Pérez, A., Benjamins, V.R. (eds.) EKAW 2002. LNCS(LNAI), vol. 2473, pp. 166–182. Springer, Heidelberg (2002)
Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nature Genetics 23, 25–29 (2000)
Horridge, M., Drummond, N., Goodwin, J., Rector, A., Stevens, R., Wang, H.: The Manchester OWL syntax. In: OWLed. (2006)
Vrandecić, D.: Explicit Knowledge Engineering Patterns with Macros. In: Welty, C., Gangemi, A. (eds.) Ontology Patterns for the Semantic Web Workshop (ISWC) (2005)
Sirin, E., Parsia, B.: SPARQL-DL: SPARQL Query for OWL-DL. In: OWLED (2007)
Aranguren, M.E., Wroe, C., Goble, C., Stevens, R.: In situ migration of handcrafted ontologies to reason-able forms. Data and Knowledge Engineering 66(1), 147–162 (2008)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Egaña, M., Rector, A., Stevens, R., Antezana, E. (2008). Applying Ontology Design Patterns in Bio-ontologies. In: Gangemi, A., Euzenat, J. (eds) Knowledge Engineering: Practice and Patterns. EKAW 2008. Lecture Notes in Computer Science(), vol 5268. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87696-0_4
Download citation
DOI: https://doi.org/10.1007/978-3-540-87696-0_4
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-87695-3
Online ISBN: 978-3-540-87696-0
eBook Packages: Computer ScienceComputer Science (R0)